So i just added a hardtop to my jeep for the first time for the colder months. And it seemed like i had a better seal fron the hard doors to the surrounds then i do to the hardtop. Top is nice a warm - less road noise but the wistle going down the highway from the lack of seal around the doors is driving me nuts. Is this just the way it is? I am only noticing it because the top makes all the road noise so much quieter? Anything i can do to help?

You can try to adjust the latch striker pin (part that latch hits on the door jam) in a little. Loosen screws and move in a little. If you go too much, the rear edge of the door will look recessed into the body.

Also have you checked the rubber seal all around the edge of the door, may be torn in places.

First thing I'd check is that you have the top fitting correctly.
Is the side by the doors sitting flush to the body .. in other words does the inner edge where the door fits to line up and seem level between top/body ?

That could be the issue. 2003 tops do not have the rear vents behind the side windows (2003 Jeeps have the vent in the rear door behind the spare tire).
Air getting thru the front heater vents has nowhere to escape out the back. If the top is sealed airtight it could cause whistling.